Biomedical subjects
Publications and source records attributed to V T Ravikumar.
High-quality oligonucleotides are obtained by selective modification of sequences containing aldehyde apurinic sites with a new chromatographic tag followed by RP-HPLC separation. Hydroxylamine derivative 1 of a water soluble nonionic surfactant modifies oligonucleotides selectively at abasic sites leading to significantly increased retention.
A triester method for the synthesis of deoxynucleoside phosphorodithioate dimers is described. The phosphorodithioate linkage is introduced using a new dithiophosphorylating reagent DPSE-SP(S)Cl(2)where DPSE = 2-diphenylmethylsilylethyl. This group is removed quickly using tetra-butylammonium fluoride leading to the quantitative formation of phosphorodithioate diesters uncontaminated with the corresponding phosphorothioates. The utility of this group is demonstrated by the synthesis of a penta-decathymidylic acid, [T(PS(2))T(PO(2))](7)T, which contains alternating phosphorodithioate/phosphate diester internucleotide linkages.
Extensive investigations on the influence of diastereomeric ratios of deoxyribonucleoside phosphoramidites on stereo-reproducibility of solid phase synthesis of phosphorothioate oligodeoxyribonucleotides via the phosphoramidite approach indicate that the process is stereoreproducible and under inherent process control.
It is demonstrated that a solution of dichloroacetic acid in toluene removes dimethoxytrityl groups from the 5'-terminus of an antisense phosphorothioate oligodeoxyribonucleotide (ISIS 5132/CGP69846A) during synthesis on solid support cleanly and efficiently. It is therefore suggested to replace health hazardous dichloromethane which is typically used in oligonucleotide synthesis as solvent for DMTr-removal by toluene.
Oligodeoxyribonucleotide phosphorothioates undergo desulfurization in presence of metal in aqueous ammonia at elevated temperatures. The extent of sulfur loss and chain cleavage have been investigated.
A series of pure fluoroquinolone antiinfective agents was prepared by multiple parallel synthesis using a simple new apparatus. These compounds were evaluated biologically against Gram-positive and Gram-negative microorganisms and against a BCG strain transfected with luciferase in a fluorescence-based antitubercular assay. Activity against relatively fast growing, acid-fast Mycobacterium smegmatis was determined in part by agar-dilution streak assays. Data obtained against Escherichia coli-derived DNA gyrase does not correlate well with whole cell assays against E. coli. These compounds were assayed by a convenient glass-fiber filter binding method modified for high throughput screening. In these analogs, the results with a N-1 cyclopropyl substituent were often inferior to those obtained with a N-1 2',4'-difluorophenyl substituent. None of the new compounds prepared was superior in its antimycobacterial potency to ciprofloxacin or temafloxacin.
2-Diphenylmethylsilylethyl (DPSE) is a new protecting group for the internucleotidic bonds in the solid-support and solution-phase synthesis of oligodeoxyribonucleotides by the phosphoramidite approach. This group is stable under acidic conditions and can be removed by a beta-fragmentation mechanism under mild conditions using aqueous NH4OH. Alternatively, this group can also be removed using tetrafluorosilane in acetonitrile.